:ב Why are we here?

תקנתם את רבו ואת עצמו לא תקנתם לישא שפחה אינו יכול בת חורין אינו יכול ליבטיל והלא לא נברא העולם אלא לפריה ורביה שנאמר לא תהו בראה לשבת יצרה

תוספות (חגיגה ב:) ד"ה לא תהו בראה. האי עשה אלים טפי מפרו ורבו כדאמר במגילה בפרק בתרא (דף כז.) מוכר אדם ס"ת לישא אשה וללמוד תורה ומייתי לא תהו בראה

Surely, the very first מצוה in the תורה is פרו ורבו. However, תוספות here indicate that the פסוק of לא תהו בראה is of some greater value. It doesn't seem that תוספות actually go into detail as to how that is, only to dispel the notion that this פסוק is used due to the absence of the real מצות פרו ורבו. 

I believe the following is the utility of the פסוק in ישעיה - either as an explanation of תוספות or an alternate approach: The main source for the מצוה is surely from בראשית. However, it is only one מצוה among 613. The פסוק in ישעיה is brought into play when the מצוה of פרו ורבו finds itself in a conflict with another מצוה, in order to establish the supremacy of the מצוה of פרו ורבו. Once we understand that the very purpose of the creation of the world was for us to inhabit it, the מצוה of פרו ורבו can take precedence over certain other מצוות.

As תוספות reference, one may sell a ספר תורה to enable the מצוה of פרו ורבו. In our case here, the emancipation of the second half of the servant is problematic with the מצוה of לעולם בהם תעבדו, prohibiting the freeing of an עבד כנעני. Neverheless, since פרו ורבו has been established as the "purpose of our creation," it is preferable to transgress לעולם בהם תעבדו or to sell a ספר תורה in order to enable its performance. 

:מ"ד Covering Your Bases

אָמַר רַב יִצְחָק בַּר אַבְדִּימִי מִשּׁוּם רַבֵּינוּ: עַל הַבֵּיעָא וְעַל מִינֵי קוּפְרָא, בַּתְּחִלָּה מְבָרֵךְ ״שֶׁהַכֹּל״, וּלְבַסּוֹף ״בּוֹרֵא נְפָשׁוֹת רַבּוֹת וְכוּ׳״. אֲבָל יַרְקָא לָא. וְרַבִּי יִצְחָק אָמַר: אֲפִילּוּ יַרְקָא, אֲבָל מַיָּא — לָא. וְרַב פָּפָּא אָמַר: אֲפִילּוּ מַיָּא.... אָמַר רַב אָשֵׁי: אֲנָא, זִמְנָא דְּכִי מִדְּכַרְנָא, עָבֵידְנָא כְּכוּלְּהוּ.

רש"י ד"ה ככולהו. אף כרב פפא:

Artscroll explains Rashi's comment: I even make a בורא נפשות on water. There are two difficulties רב אשי's statement. The first, regardless of how we understand רש"י, is the strange qualifier he uses, "when I remember." This is unusual if we are talking about פסק. Why would he not remember? But Artscroll's understanding adds some more difficulty. How can this be considered to be in accordance with all of the opinions? This is not a simple חומרא. We are dealing with ברכות. According to the first two opinions, a בורא נפשות on water is a ברכה לבטלה.

Perhaps רב אשי's statement and רש"י's comment can be understood differently. There is a way to actually act in accordance with all three opinions - two ways, actually. One can make sure never to enter the realm of uncertainty by not having enough of a vegetable or water to necessitate a ברכה אחרונה, although that would be rather difficult. Alternatively, one can make sure that whenever a vegetable or water is consumed, it is in the presence of eggs, meat, etc. which certainly require a בורא נפשות. This way, the ברכה is certainly warranted. 

This approach also accounts for the phrase זמנא דכי מדכרנא. It is not a matter of פסק דין. Rather, it is indeed a חומרא and would require extra diligence and it would be understandable that there are times when might forget to make sure to have the other items present.